ChemEnv: a fast and robust coordination environment identification tool.

Coordination or local environments have been used to describe, analyze and understand crystal structures for more than a century. Here, a new tool called ChemEnv, which can identify coordination environments in a fast and robust manner, is presented. In contrast to previous tools, the assessment of the coordination environments is not biased by small distortions of the crystal structure. Its robust and fast implementation enables the analysis of large databases of structures. The code is available open source within the pymatgen package and the software can also be used through a web app available on http://crystaltoolkit.org through the Materials Project.

Haloperoxidase Mimicry by CeO2-x Nanorods Combats Biofouling.

CeO2-x nanorods are functional mimics of natural haloperoxidases. They catalyze the oxidative bromination of phenol red to bromophenol blue and of natural signaling molecules involved in bacterial quorum sensing. Laboratory and field tests with paint formulations containing 2 wt% of CeO2-x nanorods show a reduction in biofouling comparable to Cu2 O, the most typical biocidal pigment.

M(O)V(I)P(AC): vibrational spectroscopy with a robust meta-program for massively parallel standard and inverse calculations.

We present the software package M(O)V(I)P(AC) for calculations of vibrational spectra, namely infrared, Raman, and Raman Optical Activity (ROA) spectra, in a massively parallelized fashion. M(O)V(I)P(AC) unites the latest versions of the programs SNF and AKIRA alongside with a range of helpful add-ons to analyze and interpret the data obtained in the calculations. With its efficient parallelization and meta-program design, M(O)V(I)P(AC) focuses in particular on the calculation of vibrational spectra of very large molecules containing on the order of a hundred atoms. For this purpose, it also offers different subsystem approaches such as Mode- and Intensity-Tracking to selectively calculate specific features of the full spectrum. Furthermore, an approximation to the entire spectrum can be obtained using the Cartesian Tensor Transfer Method. We illustrate these capabilities using the example of a large π-helix consisting of 20 (S)-alanine residues. In particular, we investigate the ROA spectrum of this structure and compare it to the spectra of α- and 3(10)-helical analogs.

Thermodynamics of chemical reactions with COSMO-RS: the extreme case of charge separation or recombination.

Many technically relevant chemical processes in the condensed phase involve as elementary reactive steps the formation of ions from neutral species or, as the opposite, recombination of ions. Such reactions that generate or annihilate charge defy the standard gas phase quantum chemical treatment, and also continuum solvation models are only partially able to account for the right amount of stabilization in solution. In this work, for such types of reaction, a solvation treatment involving the COSMO-RS method is assessed, which leads to improved results, i.e., errors of only around 10 kJ/mol for both protic and aprotic solvents. The examples discussed here comprise protolysis reactions and organo halide heterolysis, for both of which a comparison with reliable experimental data is possible. It is observed that for protolysis, the quality of results does not strongly depend on the quantum chemical method used for energy calculation. In contrast, in the case of heterolytic carbon-chlorine bond cleavage, clearly better results are obtained for higher correlated (coupled cluster) methods or the density functional M06-2X, which is well known for its accuracy if applied to organic chemistry. This hints at least that the right answer is obtained for the right reason and not due to a compensation of errors from gas phase thermodynamics with those from the solvation treatment. Problems encountered with certain critical solvents or upon decomposing Gibbs free energies into heats or entropies of reaction are found to relate mostly to the parameterization of the H-bonding term within COSMO-RS.

A stable six-coordinate intermediate in ammonia-dinitrogen exchange at Schrock's molybdenum catalyst.

In this work, we investigate the mechanism of the ammonia-dinitrogen exchange reaction, which is the decisive step to close the catalytic cycle of Schrock's dinitrogen reduction sequence under ambient conditions. We identify several viable pathways for the approach of dinitrogen to the five-coordinate molybdenum center of the ammonia complex by means of first-principles molecular-dynamics simulations. These exploratory simulations are then complemented by rigorous quantum-chemical structure optimizations. Our calculations have been performed for the full Schrock catalyst without simplifying the large chelate ligand, and are hence not affected by model assumptions. We show that the reaction obeys an addition-elimination mechanism via a stable six-coordinate intermediate. This intermediate has been fully characterized by stationary quantum-chemical methods. The predicted infrared spectrum of this species features an N[triple bond]N stretching vibration, which is well separated in frequency from all other N[triple bond]N stretching vibrations of N(2)-binding complexes involved in the Schrock cycle. Depending on the life time of this intermediate in the reaction liquor, the production of this intermediate might even be monitored by the absorption of the N[triple bond]N stretching vibration.

Ligands for dinitrogen fixation at Schrock-type catalysts.

Catalytic dinitrogen reduction with the Schrock complex is still hampered by low turn-over numbers that are likely to result from a degradation of the chelate ligand. In this work, we investigate modifications of the original HIPTN(3)N ligand applied by Schrock and co-workers in catalytic reduction of dinitrogen with density functional methods. We focus on ligands that are substituted in the para position of the central phenyl ring of the terphenyl moieties and on a ligand where the bridging nitrogen is exchanged by phosphorus. In addition, results for tris(pyrrolyl-alpha-methyl)amine, tris(pyrrolyl-alpha-ethyl)amine, and tris[2-(3-xylyl-imidazol-2-ylidene)ethyl]amine are reported. For this study, we take into account the full ligands without approximating them by model systems. Reaction energies for the various derivatives of HIPTN(3)N are found to be similar to those of the unchanged parent system. However, the most promising results for catalysis are obtained for the [{tris[2-(3-xylyl-imidazol-2-ylidene)ethyl]amine}Mo](N(2)) complex. Feasibility of the exchange of NH(3) by N(2) is found to be the pivotal question whether a complex can become a potential catalyst or not. A structure-reactivity relationship is derived which allows for the convenient estimation of the reaction energy for the NH(3)/N(2) exchange reaction solely from the wavenumber of the N[triple bond]N stretching vibration. This relationship may guide experiments as soon as a dinitrogen Mo complex is formed.

First-principles investigation of the Schrock mechanism of dinitrogen reduction employing the full HIPTN3N ligand.

In this work, we investigate with density functional methods mechanistic details of catalytic dinitrogen reduction mediated by Schrock's molybdenum complex under ambient conditions. We explicitly take into account the full HIPTN 3N ligand without approximating it by model systems. Our data show that replacement of the bulky HIPT substituent by smaller groups leads to deviations in energy of up to 100 kJ mol (-1). Alternatives to the Chatt-like mechanism are also investigated. It turns out that for the generation of the first molecule of ammonia, protonation of the ligand plays a crucial role. With an increasing number of hydrogens on the terminal nitrogen atom, the reduction becomes more difficult. The energetically most feasible step is the generation of the first molecule of ammonia, while the preceding transfer of the second electron and proton is the most difficult one. Reaction energies are not only reported for decamethyl chromocene as in previous studies but also for a series of other metallocenes. Furthermore, results are provided in a way to allow for a convenient estimation of the thermochemical boundary conditions of catalysis with an arbitrary combination of acid and reductant. We demonstrate that the [Mo](NNH 3) (+) complex easily loses ammonia even in the absence of a reductant. For some complexes, spin states with higher multiplicity are the ground state instead of those with lower spin multiplicity.

Formation of a unique zinc carbamate by CO2 fixation: implications for the reactivity of tetra-azamacrocycle ligated Zn(II) complexes.

The macrocyclic ligand [13]aneN 4 ( L1, 1,4,7,10-tetra-azacyclotridecane) was reacted with Zn(II) perchlorate and CO 2 in an alkaline methanol solution. It was found that, by means of subtle changes in reaction conditions, two types of complexes can be obtained: (a) the mu 3 carbonate complex 1, {[Zn( L1)] 3(mu 3-CO 3)}(ClO 4) 4, rhombohedral crystals, space group R3 c, with pentacoordinate zinc in a trigonal bipyramidal enviroment, and (b) an unprecedenced dimeric Zn(II) carbamate structure, 2, [Zn( L2)] 2(ClO 4) 2, monoclinic crystals, space group P2 1/ n. The ligand L2 (4-carboxyl-1,4,7,10-tetra-azacyclotridecane) is a carbamate derivative of L1, obtained by transformation of a hydrogen atom of one of the NH moieties into carbamate by means of CO 2 uptake. In compound 2, the distorted tetrahedral Zn(II) coordinates to the carbamate moiety in a monodentate manner. Most notably, carbamate formation can occur upon reaction of CO 2 with the [Zn L1] (2+) complex, which implicates that a Zn-N linkage is cleaved upon attack of CO 2. Since complexes of tetra-azamacrocycles and Zn(II) are routinely applied for enzyme model studies, this finding implies that the Zn-azamacrocycle moiety generally should no longer be considered to play always only an innocent role in reactions. Rather, its reactivity has to be taken into account in respective investigations. In the presence of water, 2 is transformed readily into carbonate 1. Both compounds have been additionally characterized by solid-state NMR and infrared spectroscopy. A thorough comparison of 1 with related azamacrocycle ligated zinc(II) carbonates as well as a discussion of plausible reaction paths for the formation of 2 are given. Furthermore, the infrared absorptions of the carbamate moiety have been assigned by calculating the vibrational modes of the carbamate complex using DFT methods and the vibrational spectroscopy calculation program package SNF.

The missing link in COS metabolism: a model study on the reactivation of carbonic anhydrase from its hydrosulfide analogue.

Carbonic anhydrase (CA) is known to react with carbonyl sulfide, an atmospheric trace gas, whereby H(2)S is formed. It has been shown that, in the course of this reaction, the active catalyst, the His(3)ZnOH structural motif, is converted to its hydrosulfide form: His(3)ZnOH+COS-->His(3)ZnSH+CO(2). In this study, we elucidate the mechanism of reactivation of carbonic anhydrase (CA) from its hydrosulfide analogue by using density functional calculations, a model reaction and in vivo experimental investigation. The desulfuration occurs according to the overall equation His(3)ZnSH+H(2)O right harpoon over left harpoon His(3)ZnOH+H(2)S. The initial step is a protonation equilibrium at the zinc-bound hydrosulfide. The hydrogen sulfide ligand thus formed is then replaced by a water molecule, which is subsequently deprotonated to yield the reactivated catalytic centre of CA. Such a mechanism is thought to enable a plant cell to expel H(2)S or rapidly metabolise it to cysteine via the cysteine synthase complex. The proposed mechanism of desulfuration of the hydrosulfide analogue of CA can thus be regarded as the missing link between COS consumption of plants and their sulfur metabolism.

Carbon dioxide and related heterocumulenes at zinc and lithium cations: bioinspired reactions and principles.

This Perspective starts with the discussion of the properties of an interesting metalloenzyme (carbonic anhydrase, CA) that performs extremely successfully the activation of carbon dioxide. Conclusions from that are important for many synthetic procedures and include experimental and theoretical investigation (DFT calculations) of such metal mediated processes in the condensed and in the gas phase in which the zinc cation plays a dominant role. This is extended to the bio-analogue activation of further heterocumulenes such as COS, an important atmospheric trace gas, and CS(2). Novel metal complexes which serve as useful catalysts for the reactions (copolymerisations and cyclisation) of CO(2) and oxiranes are discussed subject to the inclusion of recently published DFT calculations. We continue with the discussion of the very general aspect of the insertion of CO(2) into metal-nitrogen bonds (formation of carbamates). This again is closely related to many biological or bio-analogue processes. We describe the synthesis and mechanistic aspects of characteristic metal carbamates of a wide variety of metals and include a discussion of the mechanistic aspects, especially for the formation of Mg(2+) and Li(+) carbamates and the formation of related cyclic products after addition of the heterocumulenes CO(2), Ph-NCO or CS(2) to novel ligands, the 4H-pyridin-1-ides which finally result in the formation of e.g. 1,3-thiazole-5(2H)-thiones.

Density functional investigation of the Mitsunobu reaction.

In this article we performed an extensive density functional [BP86/6-311++G(3df,3pd) level] investigation of the hypersurface of the Mitsunobu reaction. Reaction of a phosphine with a dialkyl azodicarboxylate (first step in the Mitsunobu conversion) leads to either a five-membered oxadiazaphosphole ring (more stable) or a betaine. The subsequent formation of two stable intermediates, a dialkoxyphosphorane and an acyloxyalkoxyphosphorane, constitutes the second step in the mechanism. These intermediates are in equilibrium with each other (under exchange of alkoxy and acyloxy ligands), and both can undergo an acid-induced decomposition to yield the alkoxy- and/or acyloxyphosphonium salts. The alkoxyphosphonium salt generates the desired ester via a SN2 mechanism (inversion product). Alternatively, the phosphorus atom in a mixed acyloxyalkoxyphosphorane species can easily undergo Berry pseudorotation. A subsequent intramolecular substitution leads to the final ester via a retention mechanism. The hypersurface is much more complicated than previously assumed, and the Mitsunobu reaction is fundamentally capable of running under either inversion or retention. The possibility of selective stereocontrol is discussed. Side reactions include the formation of a degradation product and an anhydride.

How does the exchange of one oxygen atom with sulfur affect the catalytic cycle of carbonic anhydrase?

We have extended our investigations of the carbonic anhydrase (CA) cycle with the model system [(H(3)N)(3)ZnOH](+) and CO(2) by studying further heterocumulenes and catalysts. We investigated the hydration of COS, an atmospheric trace gas. This reaction plays an important role in the global COS cycle since biological consumption, that is, uptake by higher plants, algae, lichens, and soil, represents the dominant terrestrial sink for this gas. In this context, CA has been identified by a member of our group as the key enzyme for the consumption of COS by conversion into CO(2) and H(2)S. We investigated the hydration mechanism of COS by using density functional theory to elucidate the details of the catalytic cycle. Calculations were first performed for the uncatalyzed gas phase reaction. The rate-determining step for direct reaction of COS with H(2)O has an energy barrier of deltaG=53.2 kcal mol(-1). We then employed the CA model system [(H(3)N)(3)ZnOH](+) (1) and studied the effect on the catalytic hydration mechanism of replacing an oxygen atom with sulfur. When COS enters the carbonic anhydrase cycle, the sulfur atom is incorporated into the catalyst to yield [(H(3)N)(3)ZnSH](+) (27) and CO(2). The activation energy of the nucleophilic attack on COS, which is the rate-determining step, is somewhat higher (20.1 kcal mol(-1) in the gas phase) than that previously reported for CO(2). The sulfur-containing model 27 is also capable of catalyzing the reaction of CO(2) to produce thiocarbonic acid. A larger barrier has to be overcome for the reaction of 27 with CO(2) compared to that for the reaction of 1 with CO(2). At a well-defined stage of this cycle, a different reaction path can emerge: a water molecule helps to regenerate the original catalyst 1 from 27, a process accompanied by the formation of thiocarbonic acid. We finally demonstrate that nature selected a surprisingly elegant and efficient group of reactants, the [L(3)ZnOH](+)/CO(2)/H(2)O system, that helps to overcome any deactivation of the ubiquitous enzyme CA in nature.